Multiple sequence alignment - TraesCS5A01G245900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G245900 chr5A 100.000 3094 0 0 1 3094 459004899 459001806 0.000000e+00 5714.0
1 TraesCS5A01G245900 chr5A 90.909 44 4 0 2353 2396 235003624 235003581 3.330000e-05 60.2
2 TraesCS5A01G245900 chr5B 89.631 2247 162 32 298 2522 423367062 423364865 0.000000e+00 2793.0
3 TraesCS5A01G245900 chr5B 87.633 469 20 6 2664 3094 423363605 423363137 7.650000e-141 510.0
4 TraesCS5A01G245900 chr5D 92.005 738 50 7 1779 2511 358235624 358234891 0.000000e+00 1027.0
5 TraesCS5A01G245900 chr5D 90.000 520 17 11 2602 3094 358223929 358223418 9.360000e-180 640.0
6 TraesCS5A01G245900 chr7D 77.269 1113 224 21 786 1885 101799245 101798149 7.280000e-176 627.0
7 TraesCS5A01G245900 chr7D 74.119 1476 304 44 848 2267 143975929 143974476 3.510000e-149 538.0
8 TraesCS5A01G245900 chr7D 75.562 978 163 45 495 1451 631921952 631921030 2.220000e-111 412.0
9 TraesCS5A01G245900 chr7A 77.767 1057 204 19 786 1828 105778479 105777440 3.390000e-174 621.0
10 TraesCS5A01G245900 chr7A 77.364 1100 213 25 802 1885 105767615 105766536 1.220000e-173 619.0
11 TraesCS5A01G245900 chr7A 75.529 993 220 17 786 1763 146025226 146026210 1.680000e-127 466.0
12 TraesCS5A01G245900 chr7B 76.316 1216 226 43 615 1790 59180893 59179700 7.390000e-166 593.0
13 TraesCS5A01G245900 chr7B 76.264 969 178 41 504 1445 743448415 743447472 4.670000e-128 468.0
14 TraesCS5A01G245900 chr7B 79.604 505 86 12 969 1469 743457982 743457491 2.280000e-91 346.0
15 TraesCS5A01G245900 chr3D 75.332 1281 254 43 593 1833 39121091 39119833 2.690000e-155 558.0
16 TraesCS5A01G245900 chr3D 76.868 281 41 16 2010 2273 39032183 39031910 1.500000e-28 137.0
17 TraesCS5A01G245900 chr3B 76.238 1111 230 24 785 1880 61916497 61915406 2.690000e-155 558.0
18 TraesCS5A01G245900 chr3B 81.385 693 96 14 989 1653 61896885 61896198 4.540000e-148 534.0
19 TraesCS5A01G245900 chr3A 79.167 696 113 15 984 1653 50383179 50382490 1.310000e-123 453.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G245900 chr5A 459001806 459004899 3093 True 5714.0 5714 100.000 1 3094 1 chr5A.!!$R2 3093
1 TraesCS5A01G245900 chr5B 423363137 423367062 3925 True 1651.5 2793 88.632 298 3094 2 chr5B.!!$R1 2796
2 TraesCS5A01G245900 chr5D 358234891 358235624 733 True 1027.0 1027 92.005 1779 2511 1 chr5D.!!$R2 732
3 TraesCS5A01G245900 chr5D 358223418 358223929 511 True 640.0 640 90.000 2602 3094 1 chr5D.!!$R1 492
4 TraesCS5A01G245900 chr7D 101798149 101799245 1096 True 627.0 627 77.269 786 1885 1 chr7D.!!$R1 1099
5 TraesCS5A01G245900 chr7D 143974476 143975929 1453 True 538.0 538 74.119 848 2267 1 chr7D.!!$R2 1419
6 TraesCS5A01G245900 chr7D 631921030 631921952 922 True 412.0 412 75.562 495 1451 1 chr7D.!!$R3 956
7 TraesCS5A01G245900 chr7A 105777440 105778479 1039 True 621.0 621 77.767 786 1828 1 chr7A.!!$R2 1042
8 TraesCS5A01G245900 chr7A 105766536 105767615 1079 True 619.0 619 77.364 802 1885 1 chr7A.!!$R1 1083
9 TraesCS5A01G245900 chr7A 146025226 146026210 984 False 466.0 466 75.529 786 1763 1 chr7A.!!$F1 977
10 TraesCS5A01G245900 chr7B 59179700 59180893 1193 True 593.0 593 76.316 615 1790 1 chr7B.!!$R1 1175
11 TraesCS5A01G245900 chr7B 743447472 743448415 943 True 468.0 468 76.264 504 1445 1 chr7B.!!$R2 941
12 TraesCS5A01G245900 chr3D 39119833 39121091 1258 True 558.0 558 75.332 593 1833 1 chr3D.!!$R2 1240
13 TraesCS5A01G245900 chr3B 61915406 61916497 1091 True 558.0 558 76.238 785 1880 1 chr3B.!!$R2 1095
14 TraesCS5A01G245900 chr3B 61896198 61896885 687 True 534.0 534 81.385 989 1653 1 chr3B.!!$R1 664
15 TraesCS5A01G245900 chr3A 50382490 50383179 689 True 453.0 453 79.167 984 1653 1 chr3A.!!$R1 669

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
873 919 0.027979 CCTTGCCGATACACGCATTG 59.972 55.0 0.0 0.0 41.07 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2559 2760 0.104671 GCCTGAGAGAGCAAGGCTAG 59.895 60.0 5.68 0.0 39.88 3.42 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.309712 ACGATCATTGCTTTCTATCATTGG 57.690 37.500 0.00 0.00 0.00 3.16
24 25 5.824624 ACGATCATTGCTTTCTATCATTGGT 59.175 36.000 0.00 0.00 0.00 3.67
25 26 6.992123 ACGATCATTGCTTTCTATCATTGGTA 59.008 34.615 0.00 0.00 0.00 3.25
26 27 7.498900 ACGATCATTGCTTTCTATCATTGGTAA 59.501 33.333 0.00 0.00 0.00 2.85
27 28 8.013947 CGATCATTGCTTTCTATCATTGGTAAG 58.986 37.037 0.00 0.00 0.00 2.34
28 29 8.757982 ATCATTGCTTTCTATCATTGGTAAGT 57.242 30.769 0.00 0.00 0.00 2.24
29 30 9.851686 ATCATTGCTTTCTATCATTGGTAAGTA 57.148 29.630 0.00 0.00 0.00 2.24
30 31 9.851686 TCATTGCTTTCTATCATTGGTAAGTAT 57.148 29.630 0.00 0.00 0.00 2.12
48 49 9.931210 GGTAAGTATACAAGACAATTACAATGC 57.069 33.333 5.50 0.00 33.45 3.56
55 56 7.139896 ACAAGACAATTACAATGCAATACGA 57.860 32.000 0.00 0.00 0.00 3.43
56 57 7.589395 ACAAGACAATTACAATGCAATACGAA 58.411 30.769 0.00 0.00 0.00 3.85
57 58 8.243426 ACAAGACAATTACAATGCAATACGAAT 58.757 29.630 0.00 0.00 0.00 3.34
58 59 9.715123 CAAGACAATTACAATGCAATACGAATA 57.285 29.630 0.00 0.00 0.00 1.75
68 69 9.882996 ACAATGCAATACGAATATAATCACTTG 57.117 29.630 0.00 0.00 0.00 3.16
69 70 8.843733 CAATGCAATACGAATATAATCACTTGC 58.156 33.333 0.00 10.05 37.54 4.01
70 71 7.489574 TGCAATACGAATATAATCACTTGCA 57.510 32.000 13.48 13.48 42.73 4.08
71 72 7.575365 TGCAATACGAATATAATCACTTGCAG 58.425 34.615 13.48 0.00 40.84 4.41
72 73 7.017645 GCAATACGAATATAATCACTTGCAGG 58.982 38.462 11.30 0.00 37.13 4.85
73 74 7.307989 GCAATACGAATATAATCACTTGCAGGT 60.308 37.037 0.00 0.00 37.13 4.00
74 75 5.991328 ACGAATATAATCACTTGCAGGTG 57.009 39.130 22.11 22.11 38.44 4.00
80 81 2.543578 TCACTTGCAGGTGATTCGC 58.456 52.632 26.08 0.00 40.72 4.70
81 82 0.035317 TCACTTGCAGGTGATTCGCT 59.965 50.000 26.08 0.00 40.72 4.93
82 83 1.275010 TCACTTGCAGGTGATTCGCTA 59.725 47.619 26.08 3.87 40.72 4.26
83 84 1.662629 CACTTGCAGGTGATTCGCTAG 59.337 52.381 23.56 0.00 39.34 3.42
84 85 1.550524 ACTTGCAGGTGATTCGCTAGA 59.449 47.619 0.00 0.00 33.55 2.43
85 86 2.028112 ACTTGCAGGTGATTCGCTAGAA 60.028 45.455 0.00 0.00 41.13 2.10
86 87 2.760634 TGCAGGTGATTCGCTAGAAA 57.239 45.000 0.00 0.00 40.15 2.52
87 88 2.346803 TGCAGGTGATTCGCTAGAAAC 58.653 47.619 0.00 0.00 40.15 2.78
88 89 2.289382 TGCAGGTGATTCGCTAGAAACA 60.289 45.455 0.00 0.00 40.15 2.83
89 90 2.939103 GCAGGTGATTCGCTAGAAACAT 59.061 45.455 0.00 0.00 40.45 2.71
90 91 3.001736 GCAGGTGATTCGCTAGAAACATC 59.998 47.826 0.00 0.00 40.45 3.06
91 92 3.557595 CAGGTGATTCGCTAGAAACATCC 59.442 47.826 0.00 1.90 40.01 3.51
92 93 3.452627 AGGTGATTCGCTAGAAACATCCT 59.547 43.478 0.00 3.68 40.01 3.24
93 94 4.080863 AGGTGATTCGCTAGAAACATCCTT 60.081 41.667 0.00 0.00 40.01 3.36
94 95 4.271291 GGTGATTCGCTAGAAACATCCTTC 59.729 45.833 0.00 0.00 40.45 3.46
95 96 4.870426 GTGATTCGCTAGAAACATCCTTCA 59.130 41.667 0.00 0.00 40.45 3.02
96 97 5.351465 GTGATTCGCTAGAAACATCCTTCAA 59.649 40.000 0.00 0.00 40.45 2.69
97 98 5.937540 TGATTCGCTAGAAACATCCTTCAAA 59.062 36.000 0.00 0.00 40.15 2.69
98 99 6.599244 TGATTCGCTAGAAACATCCTTCAAAT 59.401 34.615 0.00 0.00 40.15 2.32
99 100 5.801350 TCGCTAGAAACATCCTTCAAATG 57.199 39.130 0.00 0.00 0.00 2.32
100 101 5.245531 TCGCTAGAAACATCCTTCAAATGT 58.754 37.500 0.00 0.00 38.98 2.71
101 102 5.705441 TCGCTAGAAACATCCTTCAAATGTT 59.295 36.000 0.00 0.00 46.53 2.71
110 111 8.871686 AACATCCTTCAAATGTTTCACTTAAC 57.128 30.769 0.00 0.00 43.08 2.01
111 112 8.006298 ACATCCTTCAAATGTTTCACTTAACA 57.994 30.769 0.00 0.00 41.81 2.41
113 114 9.132521 CATCCTTCAAATGTTTCACTTAACATC 57.867 33.333 0.00 0.00 45.44 3.06
114 115 8.463930 TCCTTCAAATGTTTCACTTAACATCT 57.536 30.769 0.00 0.00 45.44 2.90
115 116 8.567948 TCCTTCAAATGTTTCACTTAACATCTC 58.432 33.333 0.00 0.00 45.44 2.75
116 117 7.535258 CCTTCAAATGTTTCACTTAACATCTCG 59.465 37.037 0.00 0.00 45.44 4.04
117 118 6.898041 TCAAATGTTTCACTTAACATCTCGG 58.102 36.000 0.00 0.00 45.44 4.63
118 119 6.485313 TCAAATGTTTCACTTAACATCTCGGT 59.515 34.615 0.00 0.00 45.44 4.69
119 120 6.877611 AATGTTTCACTTAACATCTCGGTT 57.122 33.333 0.00 0.00 45.44 4.44
120 121 5.666969 TGTTTCACTTAACATCTCGGTTG 57.333 39.130 0.00 0.00 33.31 3.77
121 122 5.120399 TGTTTCACTTAACATCTCGGTTGT 58.880 37.500 0.00 0.00 33.31 3.32
122 123 5.587043 TGTTTCACTTAACATCTCGGTTGTT 59.413 36.000 4.44 4.44 40.30 2.83
123 124 6.094325 TGTTTCACTTAACATCTCGGTTGTTT 59.906 34.615 4.35 0.00 38.26 2.83
124 125 6.687081 TTCACTTAACATCTCGGTTGTTTT 57.313 33.333 4.35 0.00 38.26 2.43
125 126 6.687081 TCACTTAACATCTCGGTTGTTTTT 57.313 33.333 4.35 0.00 38.26 1.94
144 145 4.815040 TTTTTCCGTCGCAATTACAAGA 57.185 36.364 0.00 0.00 0.00 3.02
145 146 5.365403 TTTTTCCGTCGCAATTACAAGAT 57.635 34.783 0.00 0.00 0.00 2.40
146 147 4.335082 TTTCCGTCGCAATTACAAGATG 57.665 40.909 0.00 0.00 0.00 2.90
147 148 3.239587 TCCGTCGCAATTACAAGATGA 57.760 42.857 0.00 0.00 0.00 2.92
148 149 3.186909 TCCGTCGCAATTACAAGATGAG 58.813 45.455 0.00 0.00 0.00 2.90
149 150 2.285220 CCGTCGCAATTACAAGATGAGG 59.715 50.000 0.00 0.00 0.00 3.86
150 151 3.186909 CGTCGCAATTACAAGATGAGGA 58.813 45.455 0.00 0.00 0.00 3.71
151 152 3.616821 CGTCGCAATTACAAGATGAGGAA 59.383 43.478 0.00 0.00 0.00 3.36
152 153 4.092821 CGTCGCAATTACAAGATGAGGAAA 59.907 41.667 0.00 0.00 0.00 3.13
153 154 5.563842 GTCGCAATTACAAGATGAGGAAAG 58.436 41.667 0.00 0.00 0.00 2.62
154 155 4.635765 TCGCAATTACAAGATGAGGAAAGG 59.364 41.667 0.00 0.00 0.00 3.11
155 156 4.676546 GCAATTACAAGATGAGGAAAGGC 58.323 43.478 0.00 0.00 0.00 4.35
156 157 4.440663 GCAATTACAAGATGAGGAAAGGCC 60.441 45.833 0.00 0.00 0.00 5.19
157 158 4.591321 ATTACAAGATGAGGAAAGGCCA 57.409 40.909 5.01 0.00 40.02 5.36
158 159 2.503895 ACAAGATGAGGAAAGGCCAG 57.496 50.000 5.01 0.00 40.02 4.85
159 160 1.988107 ACAAGATGAGGAAAGGCCAGA 59.012 47.619 5.01 0.00 40.02 3.86
160 161 2.026449 ACAAGATGAGGAAAGGCCAGAG 60.026 50.000 5.01 0.00 40.02 3.35
161 162 1.963985 AGATGAGGAAAGGCCAGAGT 58.036 50.000 5.01 0.00 40.02 3.24
162 163 3.121929 AGATGAGGAAAGGCCAGAGTA 57.878 47.619 5.01 0.00 40.02 2.59
163 164 3.663198 AGATGAGGAAAGGCCAGAGTAT 58.337 45.455 5.01 0.00 40.02 2.12
164 165 3.645687 AGATGAGGAAAGGCCAGAGTATC 59.354 47.826 5.01 0.00 40.02 2.24
165 166 2.832838 TGAGGAAAGGCCAGAGTATCA 58.167 47.619 5.01 0.00 40.02 2.15
166 167 3.181329 TGAGGAAAGGCCAGAGTATCAA 58.819 45.455 5.01 0.00 40.02 2.57
167 168 3.587061 TGAGGAAAGGCCAGAGTATCAAA 59.413 43.478 5.01 0.00 40.02 2.69
168 169 4.042809 TGAGGAAAGGCCAGAGTATCAAAA 59.957 41.667 5.01 0.00 40.02 2.44
169 170 4.998051 AGGAAAGGCCAGAGTATCAAAAA 58.002 39.130 5.01 0.00 40.02 1.94
192 193 8.910351 AAAAATCTCATAGTCCATTAGCCTAC 57.090 34.615 0.00 0.00 0.00 3.18
193 194 7.863901 AAATCTCATAGTCCATTAGCCTACT 57.136 36.000 0.00 0.00 0.00 2.57
194 195 7.475137 AATCTCATAGTCCATTAGCCTACTC 57.525 40.000 0.00 0.00 0.00 2.59
195 196 5.953571 TCTCATAGTCCATTAGCCTACTCA 58.046 41.667 0.00 0.00 0.00 3.41
196 197 6.373759 TCTCATAGTCCATTAGCCTACTCAA 58.626 40.000 0.00 0.00 0.00 3.02
197 198 6.265649 TCTCATAGTCCATTAGCCTACTCAAC 59.734 42.308 0.00 0.00 0.00 3.18
198 199 5.304614 TCATAGTCCATTAGCCTACTCAACC 59.695 44.000 0.00 0.00 0.00 3.77
199 200 3.450904 AGTCCATTAGCCTACTCAACCA 58.549 45.455 0.00 0.00 0.00 3.67
200 201 3.844211 AGTCCATTAGCCTACTCAACCAA 59.156 43.478 0.00 0.00 0.00 3.67
201 202 4.288626 AGTCCATTAGCCTACTCAACCAAA 59.711 41.667 0.00 0.00 0.00 3.28
202 203 4.395231 GTCCATTAGCCTACTCAACCAAAC 59.605 45.833 0.00 0.00 0.00 2.93
203 204 4.042311 TCCATTAGCCTACTCAACCAAACA 59.958 41.667 0.00 0.00 0.00 2.83
204 205 4.764823 CCATTAGCCTACTCAACCAAACAA 59.235 41.667 0.00 0.00 0.00 2.83
205 206 5.335661 CCATTAGCCTACTCAACCAAACAAC 60.336 44.000 0.00 0.00 0.00 3.32
206 207 3.577805 AGCCTACTCAACCAAACAACT 57.422 42.857 0.00 0.00 0.00 3.16
207 208 3.898482 AGCCTACTCAACCAAACAACTT 58.102 40.909 0.00 0.00 0.00 2.66
208 209 5.043737 AGCCTACTCAACCAAACAACTTA 57.956 39.130 0.00 0.00 0.00 2.24
209 210 5.631119 AGCCTACTCAACCAAACAACTTAT 58.369 37.500 0.00 0.00 0.00 1.73
210 211 5.473504 AGCCTACTCAACCAAACAACTTATG 59.526 40.000 0.00 0.00 0.00 1.90
211 212 5.240844 GCCTACTCAACCAAACAACTTATGT 59.759 40.000 0.00 0.00 46.82 2.29
212 213 6.668323 CCTACTCAACCAAACAACTTATGTG 58.332 40.000 0.00 0.00 42.99 3.21
213 214 6.262273 CCTACTCAACCAAACAACTTATGTGT 59.738 38.462 0.00 0.00 42.99 3.72
214 215 6.131544 ACTCAACCAAACAACTTATGTGTC 57.868 37.500 0.00 0.00 42.99 3.67
215 216 5.163302 TCAACCAAACAACTTATGTGTCG 57.837 39.130 0.00 0.00 42.99 4.35
216 217 3.619233 ACCAAACAACTTATGTGTCGC 57.381 42.857 0.00 0.00 42.99 5.19
217 218 2.292292 ACCAAACAACTTATGTGTCGCC 59.708 45.455 0.00 0.00 42.99 5.54
218 219 2.570169 CAAACAACTTATGTGTCGCCG 58.430 47.619 0.00 0.00 42.99 6.46
219 220 2.157834 AACAACTTATGTGTCGCCGA 57.842 45.000 0.00 0.00 42.99 5.54
220 221 2.157834 ACAACTTATGTGTCGCCGAA 57.842 45.000 0.00 0.00 41.93 4.30
221 222 2.485903 ACAACTTATGTGTCGCCGAAA 58.514 42.857 0.00 0.00 41.93 3.46
222 223 2.873472 ACAACTTATGTGTCGCCGAAAA 59.127 40.909 0.00 0.00 41.93 2.29
223 224 3.312973 ACAACTTATGTGTCGCCGAAAAA 59.687 39.130 0.00 0.00 41.93 1.94
242 243 5.881923 AAAAAGCTATGGGCAATGATCAT 57.118 34.783 1.18 1.18 44.79 2.45
243 244 5.464030 AAAAGCTATGGGCAATGATCATC 57.536 39.130 9.06 0.00 44.79 2.92
244 245 2.708051 AGCTATGGGCAATGATCATCG 58.292 47.619 9.06 0.00 44.79 3.84
245 246 2.039480 AGCTATGGGCAATGATCATCGT 59.961 45.455 9.06 0.35 44.79 3.73
246 247 2.417933 GCTATGGGCAATGATCATCGTC 59.582 50.000 9.06 0.00 41.35 4.20
247 248 2.643995 ATGGGCAATGATCATCGTCA 57.356 45.000 9.06 6.11 0.00 4.35
248 249 2.416680 TGGGCAATGATCATCGTCAA 57.583 45.000 9.06 0.00 0.00 3.18
249 250 2.291365 TGGGCAATGATCATCGTCAAG 58.709 47.619 9.06 0.00 0.00 3.02
250 251 1.605710 GGGCAATGATCATCGTCAAGG 59.394 52.381 9.06 0.00 0.00 3.61
251 252 2.292267 GGCAATGATCATCGTCAAGGT 58.708 47.619 9.06 0.00 0.00 3.50
252 253 2.032550 GGCAATGATCATCGTCAAGGTG 59.967 50.000 9.06 1.99 0.00 4.00
253 254 2.938451 GCAATGATCATCGTCAAGGTGA 59.062 45.455 9.06 0.00 45.29 4.02
254 255 3.374988 GCAATGATCATCGTCAAGGTGAA 59.625 43.478 9.06 0.00 44.24 3.18
255 256 4.036027 GCAATGATCATCGTCAAGGTGAAT 59.964 41.667 9.06 0.00 44.24 2.57
256 257 5.237127 GCAATGATCATCGTCAAGGTGAATA 59.763 40.000 9.06 0.00 44.24 1.75
257 258 6.653183 CAATGATCATCGTCAAGGTGAATAC 58.347 40.000 9.06 0.00 44.24 1.89
258 259 5.337578 TGATCATCGTCAAGGTGAATACA 57.662 39.130 0.00 0.00 44.24 2.29
259 260 5.109210 TGATCATCGTCAAGGTGAATACAC 58.891 41.667 0.00 0.00 44.24 2.90
260 261 5.084818 ATCATCGTCAAGGTGAATACACA 57.915 39.130 0.00 0.00 44.24 3.72
261 262 4.870426 ATCATCGTCAAGGTGAATACACAC 59.130 41.667 0.00 0.00 44.24 3.82
262 263 5.568624 ATCATCGTCAAGGTGAATACACACA 60.569 40.000 0.00 0.00 44.24 3.72
263 264 6.853377 ATCATCGTCAAGGTGAATACACACAT 60.853 38.462 0.00 0.00 44.24 3.21
264 265 7.632680 ATCATCGTCAAGGTGAATACACACATA 60.633 37.037 0.00 0.00 44.24 2.29
294 295 9.710900 TGAACATAATCATATATCGTCAAAGCT 57.289 29.630 0.00 0.00 0.00 3.74
316 317 7.013220 AGCTATGGGTCATCTAGTTCATCTAA 58.987 38.462 0.00 0.00 0.00 2.10
317 318 7.677745 AGCTATGGGTCATCTAGTTCATCTAAT 59.322 37.037 0.00 0.00 0.00 1.73
319 320 7.623999 ATGGGTCATCTAGTTCATCTAATGT 57.376 36.000 0.00 0.00 0.00 2.71
323 324 6.153067 GTCATCTAGTTCATCTAATGTCCGG 58.847 44.000 0.00 0.00 0.00 5.14
329 330 4.339814 AGTTCATCTAATGTCCGGAGACTC 59.660 45.833 3.06 0.00 43.91 3.36
331 332 5.306114 TCATCTAATGTCCGGAGACTCTA 57.694 43.478 3.06 0.00 43.91 2.43
344 345 4.679106 CGGAGACTCTAGAAATGCACACAT 60.679 45.833 1.74 0.00 38.49 3.21
374 376 1.071814 TAAACACACAGGGGTCGGC 59.928 57.895 0.00 0.00 0.00 5.54
387 389 3.271490 AGGGGTCGGCTATAGTATATGGT 59.729 47.826 0.84 0.00 0.00 3.55
483 485 8.899427 AACTCGATTGATCAAATGTCATAGAT 57.101 30.769 13.09 0.00 0.00 1.98
591 593 3.493877 GCAACAACAACATAAGCATGCAA 59.506 39.130 21.98 7.96 35.39 4.08
613 616 0.395448 GGGACGAGCAGGTAGGTAGT 60.395 60.000 0.00 0.00 36.24 2.73
640 643 4.391830 AGGACAACATATGCACACGTTAAG 59.608 41.667 1.58 0.00 0.00 1.85
667 672 6.857964 AGAATAAGAACAAAACTGAATGTGCG 59.142 34.615 0.00 0.00 29.97 5.34
693 698 1.811558 GCATGGCGATGGCTTAGAGAA 60.812 52.381 10.93 0.00 39.81 2.87
758 765 4.464597 CCATAGTAGGATAAGGAGAGCCAC 59.535 50.000 0.00 0.00 36.29 5.01
770 777 2.547218 GGAGAGCCACGTTGTAAAGACA 60.547 50.000 0.00 0.00 0.00 3.41
772 781 3.740115 AGAGCCACGTTGTAAAGACAAT 58.260 40.909 0.00 0.00 46.98 2.71
796 834 7.855784 TGAAGCTATCTTTATCCATCCACTA 57.144 36.000 0.00 0.00 31.48 2.74
799 837 5.186021 AGCTATCTTTATCCATCCACTACCG 59.814 44.000 0.00 0.00 0.00 4.02
800 838 3.746045 TCTTTATCCATCCACTACCGC 57.254 47.619 0.00 0.00 0.00 5.68
844 890 6.543735 AGGTCATAAAGTGTTAAGGCTTCTT 58.456 36.000 1.30 0.00 34.65 2.52
873 919 0.027979 CCTTGCCGATACACGCATTG 59.972 55.000 0.00 0.00 41.07 2.82
877 923 1.006832 GCCGATACACGCATTGTCTT 58.993 50.000 0.00 0.00 39.91 3.01
902 949 0.693092 TAAGCGCCCCCTCCTGTATT 60.693 55.000 2.29 0.00 0.00 1.89
919 968 7.118723 TCCTGTATTCCAAGCTCATTGTATTT 58.881 34.615 0.00 0.00 37.17 1.40
921 970 7.015226 TGTATTCCAAGCTCATTGTATTTCG 57.985 36.000 0.00 0.00 37.17 3.46
924 973 4.574892 TCCAAGCTCATTGTATTTCGTCA 58.425 39.130 0.00 0.00 37.17 4.35
932 981 7.334421 AGCTCATTGTATTTCGTCAATAGTTGT 59.666 33.333 0.00 0.00 33.69 3.32
1037 1086 4.038042 TCAAGTTCAACAACAACACCAACA 59.962 37.500 0.00 0.00 34.60 3.33
1038 1087 3.908213 AGTTCAACAACAACACCAACAC 58.092 40.909 0.00 0.00 34.60 3.32
1039 1088 2.990514 GTTCAACAACAACACCAACACC 59.009 45.455 0.00 0.00 32.14 4.16
1040 1089 2.239400 TCAACAACAACACCAACACCA 58.761 42.857 0.00 0.00 0.00 4.17
1133 1184 0.668535 GTGCTCAACCCAACCTTCAC 59.331 55.000 0.00 0.00 0.00 3.18
1736 1821 0.768221 AACAGGGCTCCCTCAACTCA 60.768 55.000 4.06 0.00 46.28 3.41
1737 1822 0.548682 ACAGGGCTCCCTCAACTCAT 60.549 55.000 4.06 0.00 46.28 2.90
1742 1827 1.471676 GGCTCCCTCAACTCATGTACG 60.472 57.143 0.00 0.00 0.00 3.67
1745 1830 3.512680 CTCCCTCAACTCATGTACGTTC 58.487 50.000 0.00 0.00 0.00 3.95
2025 2149 1.904378 TCGTCGTCCATGGTGTCCA 60.904 57.895 12.58 0.00 38.19 4.02
2088 2215 0.383590 CGCCACAACAACCATTGACA 59.616 50.000 0.00 0.00 33.57 3.58
2109 2247 8.040002 TGACAGTTAATATGGGTATGGATGAA 57.960 34.615 0.00 0.00 0.00 2.57
2148 2286 4.472470 TGGTCAGATGATCCAAGACAAGAT 59.528 41.667 10.88 0.00 0.00 2.40
2288 2426 2.589540 CATTGCCCGACCTGCCTA 59.410 61.111 0.00 0.00 0.00 3.93
2300 2438 1.145819 CTGCCTAGCCTCTCTTGCC 59.854 63.158 0.00 0.00 0.00 4.52
2301 2439 1.306482 TGCCTAGCCTCTCTTGCCT 60.306 57.895 0.00 0.00 0.00 4.75
2443 2584 4.934356 ACCCTGGCTTCTGAATCAAATTA 58.066 39.130 0.00 0.00 0.00 1.40
2445 2586 5.361857 ACCCTGGCTTCTGAATCAAATTATG 59.638 40.000 0.00 0.00 0.00 1.90
2458 2599 9.859152 TGAATCAAATTATGTATACCACCATGA 57.141 29.630 0.00 0.00 0.00 3.07
2465 2606 9.561069 AATTATGTATACCACCATGAAGAAGAC 57.439 33.333 0.00 0.00 0.00 3.01
2470 2611 6.814954 ATACCACCATGAAGAAGACATACT 57.185 37.500 0.00 0.00 0.00 2.12
2471 2612 5.091261 ACCACCATGAAGAAGACATACTC 57.909 43.478 0.00 0.00 0.00 2.59
2522 2663 4.137116 AGCTACAAAATCGCACCTGATA 57.863 40.909 0.00 0.00 0.00 2.15
2524 2665 5.126067 AGCTACAAAATCGCACCTGATATT 58.874 37.500 0.00 0.00 0.00 1.28
2525 2666 5.590259 AGCTACAAAATCGCACCTGATATTT 59.410 36.000 0.00 0.00 0.00 1.40
2526 2667 6.095440 AGCTACAAAATCGCACCTGATATTTT 59.905 34.615 0.00 0.00 33.07 1.82
2541 2742 8.519526 ACCTGATATTTTTACTGCGAATTCAAA 58.480 29.630 6.22 0.00 0.00 2.69
2549 2750 7.795431 TTTACTGCGAATTCAAATTGTGATC 57.205 32.000 6.22 0.00 35.70 2.92
2550 2751 5.375417 ACTGCGAATTCAAATTGTGATCA 57.625 34.783 6.22 0.00 35.70 2.92
2554 2755 6.031471 TGCGAATTCAAATTGTGATCATCTG 58.969 36.000 6.22 0.00 35.70 2.90
2555 2756 5.457799 GCGAATTCAAATTGTGATCATCTGG 59.542 40.000 6.22 0.00 35.70 3.86
2557 2758 6.183360 CGAATTCAAATTGTGATCATCTGGGA 60.183 38.462 6.22 0.00 35.70 4.37
2559 2760 6.704289 TTCAAATTGTGATCATCTGGGATC 57.296 37.500 0.00 0.00 43.19 3.36
2561 2762 7.140522 TCAAATTGTGATCATCTGGGATCTA 57.859 36.000 0.00 0.00 43.27 1.98
2575 2777 2.315176 GGATCTAGCCTTGCTCTCTCA 58.685 52.381 0.00 0.00 40.44 3.27
2590 2792 0.031716 TCTCAGGCTAGGCAGTGGAT 60.032 55.000 19.70 0.00 0.00 3.41
2594 2796 2.280457 GCTAGGCAGTGGATCGGC 60.280 66.667 0.00 0.00 36.55 5.54
2647 3069 7.512402 TGGAAAAGACAAAAGGATAAAAGGGAT 59.488 33.333 0.00 0.00 0.00 3.85
2663 3931 1.843832 GATACCCTCCCAGAGCCCC 60.844 68.421 0.00 0.00 0.00 5.80
2664 3932 2.621672 GATACCCTCCCAGAGCCCCA 62.622 65.000 0.00 0.00 0.00 4.96
2665 3933 2.628187 ATACCCTCCCAGAGCCCCAG 62.628 65.000 0.00 0.00 0.00 4.45
2666 3934 4.421554 CCCTCCCAGAGCCCCAGA 62.422 72.222 0.00 0.00 0.00 3.86
2667 3935 2.767496 CCTCCCAGAGCCCCAGAG 60.767 72.222 0.00 0.00 0.00 3.35
2668 3936 3.478274 CTCCCAGAGCCCCAGAGC 61.478 72.222 0.00 0.00 0.00 4.09
2832 4125 4.671569 CCGCTAGCTCCATCCCGC 62.672 72.222 13.93 0.00 0.00 6.13
2838 4131 2.889521 TAGCTCCATCCCGCTCCCAA 62.890 60.000 0.00 0.00 37.68 4.12
2850 4148 0.687354 GCTCCCAACTCCAGAGAACA 59.313 55.000 0.70 0.00 0.00 3.18
2863 4161 0.601558 GAGAACACCCACGACTAGCA 59.398 55.000 0.00 0.00 0.00 3.49
2875 4193 1.009829 GACTAGCATCGCCCAACTTG 58.990 55.000 0.00 0.00 0.00 3.16
2886 4204 1.227823 CCAACTTGCTCGTGACCCA 60.228 57.895 0.00 0.00 0.00 4.51
2893 4211 1.078848 GCTCGTGACCCATTGCTCT 60.079 57.895 0.00 0.00 0.00 4.09
2897 4215 0.534412 CGTGACCCATTGCTCTCTCT 59.466 55.000 0.00 0.00 0.00 3.10
2948 4266 1.638467 GCTCATCATTCGCGACCAC 59.362 57.895 9.15 0.00 0.00 4.16
2960 4278 1.006102 CGACCACGTGAGCTTCCTT 60.006 57.895 19.30 0.00 34.56 3.36
2974 4292 3.013219 GCTTCCTTTCTCCATGTCCTTC 58.987 50.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.309712 ACCAATGATAGAAAGCAATGATCG 57.690 37.500 0.00 0.00 0.00 3.69
3 4 8.757982 ACTTACCAATGATAGAAAGCAATGAT 57.242 30.769 0.00 0.00 0.00 2.45
4 5 9.851686 ATACTTACCAATGATAGAAAGCAATGA 57.148 29.630 0.00 0.00 0.00 2.57
22 23 9.931210 GCATTGTAATTGTCTTGTATACTTACC 57.069 33.333 4.17 0.00 0.00 2.85
29 30 8.888716 TCGTATTGCATTGTAATTGTCTTGTAT 58.111 29.630 5.28 0.00 0.00 2.29
30 31 8.257830 TCGTATTGCATTGTAATTGTCTTGTA 57.742 30.769 5.28 0.00 0.00 2.41
31 32 7.139896 TCGTATTGCATTGTAATTGTCTTGT 57.860 32.000 5.28 0.00 0.00 3.16
32 33 8.619146 ATTCGTATTGCATTGTAATTGTCTTG 57.381 30.769 5.28 0.00 0.00 3.02
42 43 9.882996 CAAGTGATTATATTCGTATTGCATTGT 57.117 29.630 0.00 0.00 0.00 2.71
43 44 8.843733 GCAAGTGATTATATTCGTATTGCATTG 58.156 33.333 17.42 0.00 40.07 2.82
44 45 8.567104 TGCAAGTGATTATATTCGTATTGCATT 58.433 29.630 19.32 0.00 43.79 3.56
45 46 8.098220 TGCAAGTGATTATATTCGTATTGCAT 57.902 30.769 19.32 0.00 43.79 3.96
46 47 7.307930 CCTGCAAGTGATTATATTCGTATTGCA 60.308 37.037 20.63 20.63 45.71 4.08
47 48 7.017645 CCTGCAAGTGATTATATTCGTATTGC 58.982 38.462 16.41 16.41 40.57 3.56
48 49 8.011673 CACCTGCAAGTGATTATATTCGTATTG 58.988 37.037 10.01 0.00 40.34 1.90
49 50 7.931407 TCACCTGCAAGTGATTATATTCGTATT 59.069 33.333 14.19 0.00 41.78 1.89
50 51 7.441836 TCACCTGCAAGTGATTATATTCGTAT 58.558 34.615 14.19 0.00 41.78 3.06
51 52 6.811954 TCACCTGCAAGTGATTATATTCGTA 58.188 36.000 14.19 0.00 41.78 3.43
52 53 5.670485 TCACCTGCAAGTGATTATATTCGT 58.330 37.500 14.19 0.00 41.78 3.85
63 64 1.662629 CTAGCGAATCACCTGCAAGTG 59.337 52.381 9.27 9.27 39.20 3.16
64 65 1.550524 TCTAGCGAATCACCTGCAAGT 59.449 47.619 0.00 0.00 0.00 3.16
65 66 2.299993 TCTAGCGAATCACCTGCAAG 57.700 50.000 0.00 0.00 0.00 4.01
66 67 2.742053 GTTTCTAGCGAATCACCTGCAA 59.258 45.455 0.00 0.00 0.00 4.08
67 68 2.289382 TGTTTCTAGCGAATCACCTGCA 60.289 45.455 0.00 0.00 0.00 4.41
68 69 2.346803 TGTTTCTAGCGAATCACCTGC 58.653 47.619 0.00 0.00 0.00 4.85
69 70 3.557595 GGATGTTTCTAGCGAATCACCTG 59.442 47.826 0.00 0.00 33.14 4.00
70 71 3.452627 AGGATGTTTCTAGCGAATCACCT 59.547 43.478 0.00 0.00 33.14 4.00
71 72 3.798202 AGGATGTTTCTAGCGAATCACC 58.202 45.455 0.00 0.00 33.14 4.02
72 73 4.870426 TGAAGGATGTTTCTAGCGAATCAC 59.130 41.667 0.00 0.00 33.14 3.06
73 74 5.084818 TGAAGGATGTTTCTAGCGAATCA 57.915 39.130 0.00 0.00 34.40 2.57
74 75 6.422776 TTTGAAGGATGTTTCTAGCGAATC 57.577 37.500 0.00 0.00 0.00 2.52
75 76 6.375455 ACATTTGAAGGATGTTTCTAGCGAAT 59.625 34.615 0.00 0.00 34.18 3.34
76 77 5.705441 ACATTTGAAGGATGTTTCTAGCGAA 59.295 36.000 0.00 0.00 34.18 4.70
77 78 5.245531 ACATTTGAAGGATGTTTCTAGCGA 58.754 37.500 0.00 0.00 34.18 4.93
78 79 5.551760 ACATTTGAAGGATGTTTCTAGCG 57.448 39.130 0.00 0.00 34.18 4.26
85 86 8.474025 TGTTAAGTGAAACATTTGAAGGATGTT 58.526 29.630 0.00 0.00 46.58 2.71
86 87 8.006298 TGTTAAGTGAAACATTTGAAGGATGT 57.994 30.769 0.00 0.00 41.43 3.06
98 99 5.120399 ACAACCGAGATGTTAAGTGAAACA 58.880 37.500 0.00 0.00 43.16 2.83
99 100 5.668558 ACAACCGAGATGTTAAGTGAAAC 57.331 39.130 0.00 0.00 0.00 2.78
100 101 6.687081 AAACAACCGAGATGTTAAGTGAAA 57.313 33.333 1.76 0.00 39.98 2.69
101 102 6.687081 AAAACAACCGAGATGTTAAGTGAA 57.313 33.333 1.76 0.00 39.98 3.18
102 103 6.687081 AAAAACAACCGAGATGTTAAGTGA 57.313 33.333 1.76 0.00 39.98 3.41
123 124 4.815040 TCTTGTAATTGCGACGGAAAAA 57.185 36.364 5.72 0.00 0.00 1.94
124 125 4.452795 TCATCTTGTAATTGCGACGGAAAA 59.547 37.500 5.72 0.00 0.00 2.29
125 126 3.997681 TCATCTTGTAATTGCGACGGAAA 59.002 39.130 5.72 0.00 0.00 3.13
126 127 3.591023 TCATCTTGTAATTGCGACGGAA 58.409 40.909 3.69 3.69 0.00 4.30
127 128 3.186909 CTCATCTTGTAATTGCGACGGA 58.813 45.455 0.00 0.00 0.00 4.69
128 129 2.285220 CCTCATCTTGTAATTGCGACGG 59.715 50.000 0.00 0.00 0.00 4.79
129 130 3.186909 TCCTCATCTTGTAATTGCGACG 58.813 45.455 0.00 0.00 0.00 5.12
130 131 5.447818 CCTTTCCTCATCTTGTAATTGCGAC 60.448 44.000 0.00 0.00 0.00 5.19
131 132 4.635765 CCTTTCCTCATCTTGTAATTGCGA 59.364 41.667 0.00 0.00 0.00 5.10
132 133 4.731773 GCCTTTCCTCATCTTGTAATTGCG 60.732 45.833 0.00 0.00 0.00 4.85
133 134 4.440663 GGCCTTTCCTCATCTTGTAATTGC 60.441 45.833 0.00 0.00 0.00 3.56
134 135 4.706476 TGGCCTTTCCTCATCTTGTAATTG 59.294 41.667 3.32 0.00 35.26 2.32
135 136 4.934356 TGGCCTTTCCTCATCTTGTAATT 58.066 39.130 3.32 0.00 35.26 1.40
136 137 4.228210 TCTGGCCTTTCCTCATCTTGTAAT 59.772 41.667 3.32 0.00 35.26 1.89
137 138 3.587061 TCTGGCCTTTCCTCATCTTGTAA 59.413 43.478 3.32 0.00 35.26 2.41
138 139 3.181329 TCTGGCCTTTCCTCATCTTGTA 58.819 45.455 3.32 0.00 35.26 2.41
139 140 1.988107 TCTGGCCTTTCCTCATCTTGT 59.012 47.619 3.32 0.00 35.26 3.16
140 141 2.026449 ACTCTGGCCTTTCCTCATCTTG 60.026 50.000 3.32 0.00 35.26 3.02
141 142 2.273619 ACTCTGGCCTTTCCTCATCTT 58.726 47.619 3.32 0.00 35.26 2.40
142 143 1.963985 ACTCTGGCCTTTCCTCATCT 58.036 50.000 3.32 0.00 35.26 2.90
143 144 3.389329 TGATACTCTGGCCTTTCCTCATC 59.611 47.826 3.32 0.00 35.26 2.92
144 145 3.387962 TGATACTCTGGCCTTTCCTCAT 58.612 45.455 3.32 0.00 35.26 2.90
145 146 2.832838 TGATACTCTGGCCTTTCCTCA 58.167 47.619 3.32 0.00 35.26 3.86
146 147 3.914426 TTGATACTCTGGCCTTTCCTC 57.086 47.619 3.32 0.00 35.26 3.71
147 148 4.657814 TTTTGATACTCTGGCCTTTCCT 57.342 40.909 3.32 0.00 35.26 3.36
167 168 8.718656 AGTAGGCTAATGGACTATGAGATTTTT 58.281 33.333 0.00 0.00 37.93 1.94
168 169 8.268878 AGTAGGCTAATGGACTATGAGATTTT 57.731 34.615 0.00 0.00 37.93 1.82
169 170 7.510685 TGAGTAGGCTAATGGACTATGAGATTT 59.489 37.037 0.00 0.00 37.93 2.17
170 171 7.013220 TGAGTAGGCTAATGGACTATGAGATT 58.987 38.462 0.00 0.00 37.93 2.40
171 172 6.556639 TGAGTAGGCTAATGGACTATGAGAT 58.443 40.000 0.00 0.00 37.93 2.75
172 173 5.953571 TGAGTAGGCTAATGGACTATGAGA 58.046 41.667 0.00 0.00 37.93 3.27
173 174 6.451393 GTTGAGTAGGCTAATGGACTATGAG 58.549 44.000 0.00 0.00 37.93 2.90
174 175 5.304614 GGTTGAGTAGGCTAATGGACTATGA 59.695 44.000 0.00 0.00 37.93 2.15
175 176 5.070446 TGGTTGAGTAGGCTAATGGACTATG 59.930 44.000 0.00 0.00 37.93 2.23
176 177 5.216622 TGGTTGAGTAGGCTAATGGACTAT 58.783 41.667 0.00 0.00 37.93 2.12
177 178 4.616553 TGGTTGAGTAGGCTAATGGACTA 58.383 43.478 0.00 0.00 33.70 2.59
178 179 3.450904 TGGTTGAGTAGGCTAATGGACT 58.549 45.455 0.00 0.00 37.00 3.85
179 180 3.906720 TGGTTGAGTAGGCTAATGGAC 57.093 47.619 0.00 0.00 0.00 4.02
180 181 4.042311 TGTTTGGTTGAGTAGGCTAATGGA 59.958 41.667 0.00 0.00 0.00 3.41
181 182 4.331968 TGTTTGGTTGAGTAGGCTAATGG 58.668 43.478 0.00 0.00 0.00 3.16
182 183 5.473504 AGTTGTTTGGTTGAGTAGGCTAATG 59.526 40.000 0.00 0.00 0.00 1.90
183 184 5.631119 AGTTGTTTGGTTGAGTAGGCTAAT 58.369 37.500 0.00 0.00 0.00 1.73
184 185 5.043737 AGTTGTTTGGTTGAGTAGGCTAA 57.956 39.130 0.00 0.00 0.00 3.09
185 186 4.699925 AGTTGTTTGGTTGAGTAGGCTA 57.300 40.909 0.00 0.00 0.00 3.93
186 187 3.577805 AGTTGTTTGGTTGAGTAGGCT 57.422 42.857 0.00 0.00 0.00 4.58
187 188 5.240844 ACATAAGTTGTTTGGTTGAGTAGGC 59.759 40.000 0.00 0.00 33.74 3.93
188 189 6.262273 ACACATAAGTTGTTTGGTTGAGTAGG 59.738 38.462 0.00 0.00 36.00 3.18
189 190 7.259290 ACACATAAGTTGTTTGGTTGAGTAG 57.741 36.000 0.00 0.00 36.00 2.57
190 191 6.018588 CGACACATAAGTTGTTTGGTTGAGTA 60.019 38.462 0.00 0.00 36.00 2.59
191 192 5.220777 CGACACATAAGTTGTTTGGTTGAGT 60.221 40.000 0.00 0.00 36.00 3.41
192 193 5.204833 CGACACATAAGTTGTTTGGTTGAG 58.795 41.667 0.00 0.00 36.00 3.02
193 194 4.496673 GCGACACATAAGTTGTTTGGTTGA 60.497 41.667 0.00 0.00 36.00 3.18
194 195 3.728718 GCGACACATAAGTTGTTTGGTTG 59.271 43.478 0.00 0.00 36.00 3.77
195 196 3.243267 GGCGACACATAAGTTGTTTGGTT 60.243 43.478 0.00 0.00 36.00 3.67
196 197 2.292292 GGCGACACATAAGTTGTTTGGT 59.708 45.455 0.00 0.00 36.00 3.67
197 198 2.664424 CGGCGACACATAAGTTGTTTGG 60.664 50.000 0.00 0.00 36.00 3.28
198 199 2.222213 TCGGCGACACATAAGTTGTTTG 59.778 45.455 4.99 0.00 36.00 2.93
199 200 2.485903 TCGGCGACACATAAGTTGTTT 58.514 42.857 4.99 0.00 36.00 2.83
200 201 2.157834 TCGGCGACACATAAGTTGTT 57.842 45.000 4.99 0.00 36.00 2.83
201 202 2.157834 TTCGGCGACACATAAGTTGT 57.842 45.000 10.16 0.00 39.91 3.32
202 203 3.529634 TTTTCGGCGACACATAAGTTG 57.470 42.857 10.16 0.00 0.00 3.16
220 221 5.508489 CGATGATCATTGCCCATAGCTTTTT 60.508 40.000 10.14 0.00 44.23 1.94
221 222 4.022589 CGATGATCATTGCCCATAGCTTTT 60.023 41.667 10.14 0.00 44.23 2.27
222 223 3.504906 CGATGATCATTGCCCATAGCTTT 59.495 43.478 10.14 0.00 44.23 3.51
223 224 3.079578 CGATGATCATTGCCCATAGCTT 58.920 45.455 10.14 0.00 44.23 3.74
224 225 2.039480 ACGATGATCATTGCCCATAGCT 59.961 45.455 20.95 0.00 44.23 3.32
225 226 2.417933 GACGATGATCATTGCCCATAGC 59.582 50.000 20.95 0.00 44.14 2.97
226 227 3.667360 TGACGATGATCATTGCCCATAG 58.333 45.455 20.95 4.02 0.00 2.23
227 228 3.767902 TGACGATGATCATTGCCCATA 57.232 42.857 20.95 2.69 0.00 2.74
228 229 2.643995 TGACGATGATCATTGCCCAT 57.356 45.000 20.95 3.35 0.00 4.00
229 230 2.291365 CTTGACGATGATCATTGCCCA 58.709 47.619 20.95 16.13 0.00 5.36
230 231 1.605710 CCTTGACGATGATCATTGCCC 59.394 52.381 20.95 14.01 0.00 5.36
231 232 2.032550 CACCTTGACGATGATCATTGCC 59.967 50.000 20.95 12.15 0.00 4.52
232 233 2.938451 TCACCTTGACGATGATCATTGC 59.062 45.455 20.95 14.45 0.00 3.56
233 234 5.746307 ATTCACCTTGACGATGATCATTG 57.254 39.130 19.68 19.68 0.00 2.82
234 235 6.258727 GTGTATTCACCTTGACGATGATCATT 59.741 38.462 10.14 0.00 38.51 2.57
235 236 5.755375 GTGTATTCACCTTGACGATGATCAT 59.245 40.000 8.25 8.25 38.51 2.45
236 237 5.109210 GTGTATTCACCTTGACGATGATCA 58.891 41.667 0.00 0.00 38.51 2.92
237 238 5.005779 GTGTGTATTCACCTTGACGATGATC 59.994 44.000 0.00 0.00 43.26 2.92
238 239 4.870426 GTGTGTATTCACCTTGACGATGAT 59.130 41.667 0.00 0.00 43.26 2.45
239 240 4.242475 GTGTGTATTCACCTTGACGATGA 58.758 43.478 0.00 0.00 43.26 2.92
240 241 3.993736 TGTGTGTATTCACCTTGACGATG 59.006 43.478 0.00 0.00 43.26 3.84
241 242 4.265904 TGTGTGTATTCACCTTGACGAT 57.734 40.909 0.00 0.00 43.26 3.73
242 243 3.737032 TGTGTGTATTCACCTTGACGA 57.263 42.857 0.00 0.00 43.26 4.20
243 244 5.168569 ACTATGTGTGTATTCACCTTGACG 58.831 41.667 0.00 0.00 43.26 4.35
244 245 7.979537 TCATACTATGTGTGTATTCACCTTGAC 59.020 37.037 0.00 0.00 43.26 3.18
245 246 8.073467 TCATACTATGTGTGTATTCACCTTGA 57.927 34.615 0.00 0.00 43.26 3.02
246 247 8.604035 GTTCATACTATGTGTGTATTCACCTTG 58.396 37.037 0.00 0.00 43.26 3.61
247 248 8.318412 TGTTCATACTATGTGTGTATTCACCTT 58.682 33.333 0.00 0.00 43.26 3.50
248 249 7.847096 TGTTCATACTATGTGTGTATTCACCT 58.153 34.615 0.00 0.00 43.26 4.00
249 250 8.662781 ATGTTCATACTATGTGTGTATTCACC 57.337 34.615 0.00 0.00 43.26 4.02
268 269 9.710900 AGCTTTGACGATATATGATTATGTTCA 57.289 29.630 0.00 0.00 0.00 3.18
273 274 9.770097 CCCATAGCTTTGACGATATATGATTAT 57.230 33.333 5.65 0.00 0.00 1.28
274 275 8.758829 ACCCATAGCTTTGACGATATATGATTA 58.241 33.333 5.65 0.00 0.00 1.75
275 276 7.624549 ACCCATAGCTTTGACGATATATGATT 58.375 34.615 5.65 0.00 0.00 2.57
276 277 7.093333 TGACCCATAGCTTTGACGATATATGAT 60.093 37.037 5.65 0.00 0.00 2.45
277 278 6.210584 TGACCCATAGCTTTGACGATATATGA 59.789 38.462 5.65 0.00 0.00 2.15
278 279 6.398095 TGACCCATAGCTTTGACGATATATG 58.602 40.000 5.65 0.00 0.00 1.78
279 280 6.605471 TGACCCATAGCTTTGACGATATAT 57.395 37.500 5.65 0.00 0.00 0.86
280 281 6.437477 AGATGACCCATAGCTTTGACGATATA 59.563 38.462 5.65 0.00 0.00 0.86
281 282 4.955811 TGACCCATAGCTTTGACGATAT 57.044 40.909 5.65 0.00 0.00 1.63
282 283 4.588951 AGATGACCCATAGCTTTGACGATA 59.411 41.667 5.65 0.00 0.00 2.92
283 284 3.389329 AGATGACCCATAGCTTTGACGAT 59.611 43.478 5.65 0.00 0.00 3.73
284 285 2.766263 AGATGACCCATAGCTTTGACGA 59.234 45.455 5.65 0.00 0.00 4.20
285 286 3.185246 AGATGACCCATAGCTTTGACG 57.815 47.619 5.65 0.00 0.00 4.35
286 287 5.283457 ACTAGATGACCCATAGCTTTGAC 57.717 43.478 5.65 0.00 0.00 3.18
287 288 5.425217 TGAACTAGATGACCCATAGCTTTGA 59.575 40.000 5.65 0.00 0.00 2.69
288 289 5.674525 TGAACTAGATGACCCATAGCTTTG 58.325 41.667 0.00 0.00 0.00 2.77
289 290 5.957771 TGAACTAGATGACCCATAGCTTT 57.042 39.130 0.00 0.00 0.00 3.51
290 291 5.843421 AGATGAACTAGATGACCCATAGCTT 59.157 40.000 0.00 0.00 0.00 3.74
291 292 5.401750 AGATGAACTAGATGACCCATAGCT 58.598 41.667 0.00 0.00 0.00 3.32
292 293 5.736951 AGATGAACTAGATGACCCATAGC 57.263 43.478 0.00 0.00 0.00 2.97
293 294 8.811017 ACATTAGATGAACTAGATGACCCATAG 58.189 37.037 0.00 0.00 32.30 2.23
294 295 8.727100 ACATTAGATGAACTAGATGACCCATA 57.273 34.615 0.00 0.00 32.30 2.74
295 296 7.256475 GGACATTAGATGAACTAGATGACCCAT 60.256 40.741 0.00 0.00 33.88 4.00
296 297 6.042093 GGACATTAGATGAACTAGATGACCCA 59.958 42.308 0.00 0.00 33.88 4.51
316 317 3.068873 GCATTTCTAGAGTCTCCGGACAT 59.931 47.826 0.00 0.00 44.36 3.06
317 318 2.427453 GCATTTCTAGAGTCTCCGGACA 59.573 50.000 0.00 0.00 44.36 4.02
319 320 2.427453 GTGCATTTCTAGAGTCTCCGGA 59.573 50.000 2.93 2.93 0.00 5.14
323 324 4.569966 CCATGTGTGCATTTCTAGAGTCTC 59.430 45.833 0.00 0.00 31.99 3.36
361 362 0.032416 ACTATAGCCGACCCCTGTGT 60.032 55.000 0.00 0.00 0.00 3.72
374 376 7.939039 CCCCCATGCATTTACCATATACTATAG 59.061 40.741 0.00 0.00 0.00 1.31
387 389 2.292785 ACATTCCACCCCCATGCATTTA 60.293 45.455 0.00 0.00 0.00 1.40
459 461 9.987272 TTATCTATGACATTTGATCAATCGAGT 57.013 29.630 9.40 5.70 0.00 4.18
492 494 6.287525 TGTGCACAATATATAGCTAGCAACA 58.712 36.000 19.28 1.36 32.03 3.33
564 566 3.131933 TGCTTATGTTGTTGTTGCCTTGT 59.868 39.130 0.00 0.00 0.00 3.16
591 593 0.617820 ACCTACCTGCTCGTCCCATT 60.618 55.000 0.00 0.00 0.00 3.16
613 616 4.119136 CGTGTGCATATGTTGTCCTCATA 58.881 43.478 4.29 0.00 33.26 2.15
640 643 8.694394 GCACATTCAGTTTTGTTCTTATTCTTC 58.306 33.333 0.00 0.00 0.00 2.87
667 672 2.903855 CCATCGCCATGCCAGGTC 60.904 66.667 0.00 0.00 0.00 3.85
680 685 4.640789 TCTCGAACTTCTCTAAGCCATC 57.359 45.455 0.00 0.00 36.05 3.51
688 693 5.465935 GTGATCAGTTTCTCGAACTTCTCT 58.534 41.667 0.00 0.00 46.34 3.10
758 765 8.230486 AAAGATAGCTTCATTGTCTTTACAACG 58.770 33.333 0.00 0.00 39.89 4.10
770 777 7.753630 AGTGGATGGATAAAGATAGCTTCATT 58.246 34.615 0.00 0.00 31.82 2.57
772 781 6.753913 AGTGGATGGATAAAGATAGCTTCA 57.246 37.500 0.00 0.00 31.82 3.02
783 820 3.162666 CCTAGCGGTAGTGGATGGATAA 58.837 50.000 19.56 0.00 0.00 1.75
796 834 4.400120 TGTTTAATTTGGTTCCTAGCGGT 58.600 39.130 0.00 0.00 0.00 5.68
799 837 6.755206 ACCTTTGTTTAATTTGGTTCCTAGC 58.245 36.000 0.00 0.00 0.00 3.42
800 838 7.947282 TGACCTTTGTTTAATTTGGTTCCTAG 58.053 34.615 0.00 0.00 0.00 3.02
873 919 4.001652 GAGGGGGCGCTTAAATATAAGAC 58.998 47.826 7.64 0.00 40.90 3.01
877 923 2.304761 CAGGAGGGGGCGCTTAAATATA 59.695 50.000 7.64 0.00 0.00 0.86
902 949 4.574892 TGACGAAATACAATGAGCTTGGA 58.425 39.130 0.00 0.00 39.30 3.53
919 968 9.516314 CATAGAGATGTAAACAACTATTGACGA 57.484 33.333 0.00 0.00 0.00 4.20
921 970 8.552034 GCCATAGAGATGTAAACAACTATTGAC 58.448 37.037 0.00 0.00 0.00 3.18
924 973 6.706270 CGGCCATAGAGATGTAAACAACTATT 59.294 38.462 2.24 0.00 0.00 1.73
932 981 2.037251 GAGGCGGCCATAGAGATGTAAA 59.963 50.000 23.09 0.00 0.00 2.01
1037 1086 1.187087 CGAAGGGAGCTCTAGTTGGT 58.813 55.000 14.64 0.00 0.00 3.67
1148 1199 4.372656 GTTCTTATTCAGATCCACCTCCG 58.627 47.826 0.00 0.00 0.00 4.63
1525 1590 4.320714 GGCGTGTTCATGATTCATATGCAT 60.321 41.667 3.79 3.79 0.00 3.96
1699 1784 1.759445 GTTGCTGCTCTCCTCCTATGA 59.241 52.381 0.00 0.00 0.00 2.15
1703 1788 1.551908 CCTGTTGCTGCTCTCCTCCT 61.552 60.000 0.00 0.00 0.00 3.69
1742 1827 3.407967 TCCATGGGAGGCGGGAAC 61.408 66.667 13.02 0.00 0.00 3.62
1745 1830 2.445845 TAGTCCATGGGAGGCGGG 60.446 66.667 13.02 0.00 29.39 6.13
1845 1930 3.869272 CAAGCTGCCCGTCATCGC 61.869 66.667 0.00 0.00 35.54 4.58
2025 2149 3.382832 CCGGTCAACGCCCTCTCT 61.383 66.667 0.00 0.00 42.52 3.10
2046 2173 2.010582 TTGCCTTGGACGTTGTTGCC 62.011 55.000 0.00 0.00 0.00 4.52
2088 2215 9.300681 CACATTTCATCCATACCCATATTAACT 57.699 33.333 0.00 0.00 0.00 2.24
2109 2247 4.532126 TCTGACCATGAGTACTTCCACATT 59.468 41.667 0.00 0.00 0.00 2.71
2161 2299 4.581409 TGGATGGTTGATTCATGCATACAG 59.419 41.667 0.00 0.00 37.89 2.74
2218 2356 0.873743 AAAACGCGGTGCAAACCATG 60.874 50.000 12.47 0.00 0.00 3.66
2219 2357 0.669077 TAAAACGCGGTGCAAACCAT 59.331 45.000 12.47 0.00 0.00 3.55
2233 2371 4.098416 GCGATCATGCTGGAAAGTAAAAC 58.902 43.478 0.00 0.00 0.00 2.43
2282 2420 1.145819 GGCAAGAGAGGCTAGGCAG 59.854 63.158 19.70 2.13 0.00 4.85
2346 2484 7.485810 AGACGGTTTTGCAGTTTAAATAACTT 58.514 30.769 0.00 0.00 0.00 2.66
2348 2486 7.688478 AAGACGGTTTTGCAGTTTAAATAAC 57.312 32.000 0.00 0.00 0.00 1.89
2352 2490 9.968870 AAATATAAGACGGTTTTGCAGTTTAAA 57.031 25.926 0.00 0.00 0.00 1.52
2355 2493 9.005777 TCTAAATATAAGACGGTTTTGCAGTTT 57.994 29.630 0.00 0.00 0.00 2.66
2410 2549 3.593780 AGAAGCCAGGGTTATTCTCCTTT 59.406 43.478 3.13 0.00 0.00 3.11
2443 2584 6.560003 TGTCTTCTTCATGGTGGTATACAT 57.440 37.500 5.01 0.00 0.00 2.29
2445 2586 7.727181 AGTATGTCTTCTTCATGGTGGTATAC 58.273 38.462 0.00 0.00 0.00 1.47
2470 2611 7.707624 TTTAGTCTTCCCTGTTTATACGAGA 57.292 36.000 0.00 0.00 0.00 4.04
2471 2612 8.943909 ATTTTAGTCTTCCCTGTTTATACGAG 57.056 34.615 0.00 0.00 0.00 4.18
2522 2663 8.586570 TCACAATTTGAATTCGCAGTAAAAAT 57.413 26.923 2.79 0.00 0.00 1.82
2524 2665 7.864882 TGATCACAATTTGAATTCGCAGTAAAA 59.135 29.630 2.79 0.00 37.92 1.52
2525 2666 7.366513 TGATCACAATTTGAATTCGCAGTAAA 58.633 30.769 2.79 0.00 37.92 2.01
2526 2667 6.907741 TGATCACAATTTGAATTCGCAGTAA 58.092 32.000 2.79 0.00 37.92 2.24
2541 2742 4.019501 GGCTAGATCCCAGATGATCACAAT 60.020 45.833 0.00 0.00 42.95 2.71
2549 2750 1.698532 AGCAAGGCTAGATCCCAGATG 59.301 52.381 0.00 0.00 36.99 2.90
2550 2751 1.977129 GAGCAAGGCTAGATCCCAGAT 59.023 52.381 0.00 0.00 39.88 2.90
2554 2755 1.618343 GAGAGAGCAAGGCTAGATCCC 59.382 57.143 0.00 0.00 39.88 3.85
2555 2756 2.297033 CTGAGAGAGCAAGGCTAGATCC 59.703 54.545 0.00 0.00 39.88 3.36
2557 2758 2.318908 CCTGAGAGAGCAAGGCTAGAT 58.681 52.381 0.00 0.00 39.88 1.98
2559 2760 0.104671 GCCTGAGAGAGCAAGGCTAG 59.895 60.000 5.68 0.00 39.88 3.42
2561 2762 2.988800 GCCTGAGAGAGCAAGGCT 59.011 61.111 5.68 0.00 43.88 4.58
2575 2777 2.136878 CCGATCCACTGCCTAGCCT 61.137 63.158 0.00 0.00 0.00 4.58
2647 3069 3.289211 TGGGGCTCTGGGAGGGTA 61.289 66.667 0.00 0.00 0.00 3.69
2663 3931 1.828768 GAGATGGACTGGGGCTCTG 59.171 63.158 0.00 0.00 0.00 3.35
2664 3932 1.760086 CGAGATGGACTGGGGCTCT 60.760 63.158 0.00 0.00 0.00 4.09
2665 3933 2.818132 CGAGATGGACTGGGGCTC 59.182 66.667 0.00 0.00 0.00 4.70
2666 3934 3.474570 GCGAGATGGACTGGGGCT 61.475 66.667 0.00 0.00 0.00 5.19
2667 3935 4.554036 GGCGAGATGGACTGGGGC 62.554 72.222 0.00 0.00 0.00 5.80
2668 3936 2.669133 TTGGCGAGATGGACTGGGG 61.669 63.158 0.00 0.00 0.00 4.96
2669 3937 1.450312 GTTGGCGAGATGGACTGGG 60.450 63.158 0.00 0.00 0.00 4.45
2670 3938 1.811266 CGTTGGCGAGATGGACTGG 60.811 63.158 0.00 0.00 41.33 4.00
2671 3939 1.811266 CCGTTGGCGAGATGGACTG 60.811 63.158 0.00 0.00 41.33 3.51
2832 4125 1.002544 GGTGTTCTCTGGAGTTGGGAG 59.997 57.143 0.00 0.00 0.00 4.30
2838 4131 0.469331 TCGTGGGTGTTCTCTGGAGT 60.469 55.000 0.00 0.00 0.00 3.85
2850 4148 2.494918 GCGATGCTAGTCGTGGGT 59.505 61.111 4.86 0.00 43.27 4.51
2863 4161 2.034879 CACGAGCAAGTTGGGCGAT 61.035 57.895 4.75 0.00 36.08 4.58
2875 4193 1.078848 AGAGCAATGGGTCACGAGC 60.079 57.895 1.37 0.00 43.97 5.03
2893 4211 0.103755 CAAGATGCGGCTGCTAGAGA 59.896 55.000 20.27 0.00 43.34 3.10
2948 4266 2.005451 CATGGAGAAAGGAAGCTCACG 58.995 52.381 0.00 0.00 32.83 4.35
2974 4292 3.197790 CTCATGTCCGCCTTGCCG 61.198 66.667 0.00 0.00 0.00 5.69


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.